In the past I would spot check them and there were plenty of submissions that were neither bot submitted nor obviously rule breaking that were deleted. My best guess was that mods of sufficiently large subreddits just like to shape the content that's shown. In most places, there seems to neither be the power user nepotism of late-era Digg nor the Eastern Germany level narrative censorship of subs like worldnews. Rather it just seems like a ton of cooks in the kitchen (huge modlists) with some of the mods seeming to just take action for action's sake. Either way the point is that users aren't really dictating the content.

Don't even get me started about local city subreddit busybody moderators with their online fiefdoms and their "Daily Discussion" post graveyards.